Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (CS.CL) 2026-06-18

Phonikud: Overcoming Phonetic Underspecification for Hebrew Text-To-Speech

Text-to-speech (TTS) for Modern Hebrew is challenged by the language's orthographic complexity, with existing solutions ignoring underspecified phonetic features such as stress. We present a framework for more phonetically accurate Hebrew TTS with four contributions: (1) Phonikud, an open-source Hebrew grapheme-to-phoneme (G2P) system that outputs fully-specified International Phonetic Alphabet (IPA) transcriptions, designed by augmenting a base diacritizer. (2) The ILSpeech corpus of paired Hebrew audio, text, and expert IPA annotations. (3) A benchmark for the previously unmeasured task of Hebrew G2P conversion. (4) Hebrew audio-to-IPA models capturing previously disregarded phonetic details for automatic TTS evaluation. Our results show that Phonikud more accurately predicts Hebrew phonemes than prior methods, and that small, local TTS models with phonetic input from Phonikud approach large proprietary systems. We release our code, data, and models at https://phonikud.github.io.

02.
arXiv (CS.LG) 2026-06-16

Exact Federated Continual Unlearning for Ridge Heads on Frozen Foundation Models

arXiv:2603.12977v3 Announce Type: replace Abstract: Foundation models are commonly deployed as frozen feature extractors with a small trainable head to adapt to private, user-generated data in federated settings. The ``right to be forgotten'' requires removing the influence of specific samples or users from the trained model on demand. Existing federated unlearning methods target general deep models and rely on approximate reconstruction or selective retraining, making exactness costly or elusive. We study this problem in a practically relevant but under-explored regime: a frozen foundation model with a ridge-regression head. The exact optimum depends on the data only through two additive sufficient statistics, which we turn into a communication protocol supporting an arbitrary stream of add and delete requests via fixed-size messages. The server maintains a head that is, in exact arithmetic, pointwise identical to centralized retraining after every request. We provide deterministic retrain-equivalence guarantees, order and partition invariance, two server-side variants, and a Bayesian certificate of zero KL divergence. Experiments on four benchmarks confirm the guarantees: both variants match centralized ridge retraining to within $10^{-9}$ relative Frobenius error and complete each request at orders-of-magnitude lower cost than federated retraining baselines.

03.
arXiv (CS.CV) 2026-06-16

Improved Knowledge Distillation for Land-Use Image Classification

In the present article, an improved Knowledge Distillation (KD) framework has been proposed for efficient compression of deep convolutional neural networks for land-use image classification task. Motivated by the need to achieve competitive classification accuracy while reducing computational complexity, a teacher-student learning paradigm is adopted in which a VGG16 network transfers knowledge to a lightweight MobileNetV2 model. The proposed framework integrates hard supervision from ground truth labels with a soft supervision strategy that combines Kullback-Leibler divergence and Cosine Similarity losses. Experiments conducted on three land-use datasets show that the proposed KD-based method yields improved performance, and achieves an accuracy of 99.04%, outperforming both baseline student training and single-loss distillation approaches, while retaining substantial model compression.

04.
arXiv (CS.AI) 2026-06-17

Brep2Shape: Boundary and Shape Representation Alignment via Self-Supervised Transformers

arXiv:2602.07429v2 Announce Type: replace-cross Abstract: Boundary representation (B-rep) is the industry standard for computer-aided design (CAD). While deep learning shows promise in processing B-rep models, existing methods suffer from a representation gap: continuous approaches offer analytical precision but are visually abstract, whereas discrete methods provide intuitive clarity at the expense of geometric precision. To bridge this gap, we introduce Brep2Shape, a novel self-supervised pre-training method designed to align abstract boundary representations with intuitive shape representations. Our method employs a geometry-aware task where the model learns to predict dense spatial points from parametric Bézier control points, enabling the network to better understand physical manifolds derived from abstract coefficients. To enhance this alignment, we propose a Dual Transformer backbone with parallel streams that independently encode surface and curve tokens to capture their distinct geometric properties. Moreover, the topology attention is integrated to model the interdependencies between surfaces and curves, thereby maintaining topological consistency. Experimental results demonstrate that Brep2Shape offers significant scalability, achieving state-of-the-art accuracy and faster convergence across various downstream tasks.Code is available at this repository: https://github.com/thuml/Brep2Shape.

05.
arXiv (quant-ph) 2026-06-15

Quantum sensing through bosonic-fermionic Bell-state transitions in two-photon interference

arXiv:2606.14408v1 Announce Type: new Abstract: Hong-Ou-Mandel (HOM) interference has become a central resource for quantum sensing and metrology owing to its sensitivity to temporal delay and photon indistinguishability. However, existing HOM-based sensing schemes generally rely on inserting a sample into one arm of the interferometer, making the measurement vulnerable to optical loss, alignment instability, and bandwidth-dependent distortion of the interference profile. Here, we demonstrate a symmetry-controlled quantum sensing scheme based on continuous transitions between symmetric (bosonic-like) and antisymmetric (fermionic-like) Bell states in two-photon interference. By imprinting a geometric phase onto the classical pump beam and transferring it to polarization-entangled photons generated via spontaneous parametric down-conversion, we coherently tune the exchange symmetry of the entangled state without altering the temporal or spectral indistinguishability of the photons. The HOM response evolves continuously from bunching to antibunching with a sine square phase dependence, producing a coincidence modulation of approximately 10 * 10^4 counts s^-1 counts/s. In contrast to conventional HOM sensing, the phase-modulation linewidth remains fixed at pi/2, independent of photon bandwidth. Using a birefringent crystal placed directly in the pump beam, we measure thermo-dispersive birefringence with a resolution of the order of 10^{-6} over a broad temperature range. Our results establish exchange symmetry as a controllable resource for robust quantum sensing and symmetry-engineered photonic quantum information processing.

06.
arXiv (CS.AI) 2026-06-19

ScaffoldAgent: Utility-Guided Dynamic Outline Optimization for Open-Ended Deep Research

arXiv:2606.20122v1 Announce Type: new Abstract: Open-ended deep research (OEDR) requires systems to acquire knowledge through multi-round retrieval and generate coherent long-form reports. The outline plays a central role as a structural scaffold that coordinates retrieval, evidence organization, and generation. However, existing methods either fix the outline before writing or refine it with local heuristics, leading to scaffold drift under continuous information accumulation and delayed feedback for evaluating outline modifications. We propose ScaffoldAgent, a utility-guided dynamic outline optimization framework for OEDR. ScaffoldAgent models outline evolution as a structured decision process with three operations: Expansion, Contraction, and Revision, enabling controlled updates to the report scaffold. It further introduces a utility-guided feedback mechanism that estimates the downstream value of each outline operation from retrieval gain, structural coherence, and trial-generation quality. The resulting utility signal guides node selection, operation scheduling, and termination during inference. Experiments on DeepResearch Bench and DeepResearch Gym show that ScaffoldAgent consistently improves long-form report generation and factual grounding over existing deep research agents.

07.
arXiv (quant-ph) 2026-06-12

Trading symmetry for Hilbert-space dimension in Bell-inequality violation

arXiv:2601.02893v3 Announce Type: replace Abstract: In quantum information, asymmetry, i.e., the lack of symmetry, is a resource allowing one to accomplish certain tasks that are otherwise impossible. Similarly, in a Bell test using any given Bell inequality, the maximum violation achievable using quantum strategies respecting or disregarding a certain symmetry can be different. In this work, we focus on the symmetry involved in the exchange of parties and explore when we have to trade this symmetry for a lower-dimensional quantum strategy in achieving the maximal violation of given Bell inequalities. For the family of symmetric Collins-Gisin-Linden-Massar-Popescu inequalities, we provide evidence showing that there is no such trade-off. However, for several other Bell inequalities with a small number of dichotomic measurement settings, we show that symmetric quantum strategies in the minimal Hilbert space dimension can only lead to a suboptimal Bell violation. In other words, there exist symmetric Bell inequalities that can only be maximally violated by asymmetric quantum strategies of minimal dimension. In contrast, one can also find examples of asymmetric Bell inequalities that are maximally violated by symmetric correlations. The implications of these findings on the geometry of the set of quantum correlations and the possibility of performing self-testing therefrom are briefly discussed.

08.
arXiv (CS.LG) 2026-06-16

GPT-Based Fast Simulation of CLAS12 Detector Hits via Conditional Autoregressive Generation

arXiv:2606.16035v1 Announce Type: cross Abstract: Modern particles physics experiments have demonstrated an increasing need for fast, high-fidelity detector simulation as detector components have improved and subsequent computational requirements approach the limits of available resources. Recently, deep generative models have emerged as a promising alternative to traditional Monte-Carlo methods, with recent works drawing inspiration from large language models (LLMs) and self-supervised next-token prediction methods. In this work, we present an application of a GPT-style autoregressive transformer as a fast surrogate model for the calorimeter inside the CLAS12 experiment at the Thomas Jefferson National Accelerator Facility. The model is conditioned on incident momentum and generates realistic detector hits autoregressively across all nine calorimeter layers as sequences of strip, ADC, and TDC tokens. We demonstrate that the model faithfully reproduces hit multiplicity, spatial distributions, energy deposits, and the energy-momentum response of the electromagnetic calorimeter. The generator achieves inference rates exceeding 700 events per second on a single GPU, providing a substantial speedup over traditional Geant4-based simulations while maintaining physics fidelity essential for high-luminosity experimental programs.

09.
arXiv (math.PR) 2026-06-16

Hua-Chen New Theory of Economic Optimization

arXiv:2504.19134v4 Announce Type: replace-cross Abstract: Between 1957-1985, Chinese mathematician Loo-Keng Hua pioneered economic optimization theory through three key contributions: establishing economic stability's fundamental theorem, proving the uniqueness of equilibrium solutions in economic systems, and developing a consumption-integrated model 50 days before his death. Since 1988, Mu-Fa Chen has been working on Hua's theory. He introduced stochastics, namely Markov chains, to economic optimization theory. He updated and developed Hua's model and came up with a new model (Chen's model) which has become the starting point of a new economic optimization theory. Chen's theory can be applied to economic stability test, bankruptcy prediction, product ranking and classification, economic prediction and adjustment, economic structure optimization. Chen's theory can also provide efficient algorithms that are programmable and intelligent. {Stochastics} is the cornerstone of Chen's theory. There is no overlap between Chen's theory, and the existing mathematical economy theory and the economics developments that were awarded Nobel Prizes in Economics between 1969 and 2024. The distinguished features of Chen's theory from the existing theories are quantitative, calculable, predictable, optimizable, programmable and can be intelligent. This survey provides a theoretical overview of the newly published monograph [5rw24]. Specifically, the invariant of the economic structure matrix, also known as the Chen's invariant, was first published in this survey.

10.
medRxiv (Medicine) 2026-06-22

Leishmaniasis on YouTube: a critical appraisal of the quality, reliability, and transparency of educational content

Background: Leishmaniasis is a neglected tropical disease of significant global public health importance, for which accurate information is essential to support prevention and early care-seeking, particularly in endemic, resource-limited settings. YouTube is a widely used source of health information, but the quality and reliability of leishmaniasis-related content have not been evaluated. We aimed to assess the quality, reliability, and transparency of English-language YouTube videos on leishmaniasis. Methods: We conducted a cross-sectional analysis of YouTube videos retrieved via the YouTube Data API on 15 June 2026 using the terms "leishmaniasis," "cutaneous leishmaniasis," and "visceral leishmaniasis." After applying eligibility criteria and screening the 150 most-viewed eligible videos, 48 videos were included. Two reviewers independently assessed each video using the modified DISCERN (mDISCERN) tool, the Global Quality Score (GQS), and the JAMA benchmark criteria, with disagreements resolved by consensus. Inter-rater agreement was assessed using the intraclass correlation coefficient (ICC), and associations were examined using Spearman's rank correlation. Results: Of 402 videos retrieved, 48 met the inclusion criteria. The median GQS was 3.00 (IQR 2.00-4.00) and median mDISCERN was 3.00 (IQR 2.38-4.50), indicating moderate quality and reliability, while the median JAMA score was 2.00 (IQR 1.00-2.00), reflecting limited transparency; no video met all four JAMA criteria. The overwhelming majority of videos (47/48, 97.9%) were of professional or institutional origin. Inter-rater agreement was good to excellent (ICC 0.883 for GQS, 0.896 for mDISCERN, 1.000 for JAMA). The instruments were strongly inter-correlated (mDISCERN-GQS rho = 0.841, p < 0.001). Quality scores did not correlate positively with views, likes, or video duration; comments correlated weakly and negatively with mDISCERN (rho = -0.337, p = 0.031) and JAMA (rho = -0.381, p = 0.014). Conclusions: YouTube videos on leishmaniasis are of moderate quality and reliability but limited transparency, and are produced almost exclusively by professional sources. Video popularity, length, and age were not indicators of quality. There is a need for experts and institutions to produce clearly authored, well-sourced, and transparent educational content on this neglected tropical disease.

11.
arXiv (quant-ph) 2026-06-11

Quest for quantum advantage: Monte Carlo wave-function simulations of the Coherent Ising Machine

arXiv:2501.02681v2 Announce Type: replace Abstract: The Coherent Ising Machine (CIM) is a quantum network of optical parametric oscillators (OPOs) intended to find ground states of the Ising model. This is an NP-hard problem, related to several important minimization problems, including the max-cut graph problem. In order to enhance its potential performance, we analyze the coherent coupling strategy for the CIM in a highly quantum regime. To explore this limit, without assuming gaussianity, we employ accurate numerical simulations. Due to the inherent complexity of the system, the maximum network size is limited. While master equation methods can be used, their scalability diminishes rapidly for larger systems. Instead, we use Monte Carlo wave-function methods, which scale as the wave-function dimension, and use large numbers of samples. These simulations involve Hilbert spaces exceeding $10^{7}$ dimensions. To evaluate success probabilities, we use quadrature probabilities. We demonstrate the potential for quantum computational advantage by reducing the time required to reach maximum success probability in a low-dissipation regime enabled by initial quantum superpositions and entanglement. Furthermore, we demonstrate that tailored time-dependent couplings can amplify these quantum effects. Comparisons with classical CIM models give evidence that quantum tunneling effects in this strong coupling limit can overcome trapping in false minima. This can greatly increase success rates, indicating a potential for quantum advantage. Finally, we perform a coherence analysis based on the state purity to examine the role of quantum coherence in CIM performance and to determine how state purity correlates with improved optimization outcomes.

12.
arXiv (CS.CV) 2026-06-18

Physics-IQ Verified

Video generative models ( VGMs) have become a new frontier that can be used not just for video generation but for a multitude of downstream tasks, including world modeling. To advance these tasks, a good video model must understand the physical reality of the world. Evaluating this understanding is an emerging field and has led to the Physics-IQ benchmark, which quantifies this explicitly by comparing model-generated videos to real-world videos of physical experiments. In this work, we present a systematic audit of the Physics-IQ benchmark, expose shortcomings and propose three solutions that sharpen how we can measure physical understanding of VGMs. Specifically, we improve prompt and ground-truth quality to reduce the influence of confounding factors and further introduce a sample-level scoring system that weights each sample and metric equally. Our resulting benchmark, Physics-IQ Verified, refines 57.6\% of all samples and improves over 34.8\% of prompts. In a comparison study using six image-to-video generative models, we observe moderate but meaningful ranking changes (Kendall's $\tau = 0.46$). We hope Physics-IQ Verified advances the community by providing a more reliable signal toward physically accurate VGMs. The code for the benchmark can be accessed at https://github.com/google-deepmind/physics-iq-benchmark

13.
arXiv (CS.AI) 2026-06-18

SHIFT: Semantic Harmonization via Index-side Feature Transformation for Multilingual Information Retrieval

arXiv:2606.18801v1 Announce Type: cross Abstract: With the rapid expansion of massive multilingual corpora, Multilingual Information Retrieval (MLIR) has emerged as a critical technology for global information access. MLIR enables users to retrieve semantically relevant documents from multilingual text collections using a single-language query. However, recent multilingual dense retrieval models often exhibit a strong preference for documents in the same language as the query. This leads to severe language bias, where top-ranked results are dominated by documents of specific languages, even when documents in other languages contain more semantically relevant information. To address this issue, we propose SHIFT, a training-free method applicable in the indexing stage. Specifically, SHIFT utilizes parallel translation pairs to estimate a relative language vector for each target language with respect to a source language. Subsequently, SHIFT corrects the language-specific offset by subtracting this relative language vector from document embeddings during indexing. Our comprehensive evaluation across four MLIR benchmarks and diverse dense retrieval models confirms that SHIFT can effectively mitigate language bias and enhance MLIR performance.

14.
arXiv (CS.LG) 2026-06-18

EfficientRollout: System-Aware Self-Speculative Decoding for RL Rollouts

arXiv:2606.18967v1 Announce Type: new Abstract: Reinforcement learning (RL) has become a representative post-training paradigm for LLMs, enabling strong reasoning and agentic capabilities. However, rollout generation remains a dominant latency bottleneck because autoregressive sampling decodes responses sequentially and a small number of long-tailed generations often determine completion time. Speculative decoding (SD) offers a natural way to address this bottleneck, as it is a well-established technique for serving fixed LLMs that reduces latency by rapidly drafting tokens and accepting them through parallel verification while preserving the target-model distribution. However, its practical speedups do not directly carry over to RL rollouts: (i) the evolving target policy makes any fixed drafter increasingly mismatched with the policy's output distribution; and (ii) active batch sizes shrink throughout rollout decoding, shifting decoding from compute-bound to memory-bound regimes where parallel verification can exploit underutilized compute. Therefore, accelerating RL rollouts requires both a drafter that remains effective under long, high-temperature generations from an evolving policy and system-aware use of SD that avoids compute-bound regimes. We present EfficientRollout, a system-aware self-SD framework designed to address this gap for RL rollouts. EfficientRollout induces a quantized drafter from the target model (i.e. self-speculative decoding), keeping it coupled to the evolving policy without separate drafter pretraining or online adaptation. It further coordinates a system-aware SD toggle policy with acceptance-aware draft-length adaptation, enabling speculation only in beneficial regimes while matching the drafting budget to evolving drafter quality. EfficientRollout reduces rollout and end-to-end latency by up to 19.6% and 12.7%, respectively, over an accelerated AR rollout baseline, while preserving final model quality.

15.
arXiv (quant-ph) 2026-06-16

Information Is Not Physical: Possibility Spaces, Erasure, and the Structure of Unrealized Alternatives

arXiv:2606.15120v1 Announce Type: cross Abstract: The slogan ``information is physical,'' introduced by Rolf Landauer and developed through quantum information theory and black-hole thermodynamics, has achieved near-axiomatic status in modern physics. Yet the ontological status of information remains surprisingly underexamined: most discussions either reduce information to a form of energy or treat it as a purely mathematical object. This paper proposes a third position. I argue that information is neither a physical substance nor a free-floating abstraction, but rather the structure of physically realizable alternatives – a counterfactual structure that a physical system instantiates in virtue of the possibility space available to it. Building on Shannon's combinatorial definition, the Landauer principle, the no-cloning theorem, and the black-hole information paradox, I show that the informational content of any physical event is constituted by the set of outcomes that could have occurred but did not. This counterfactual reading dissolves several persistent confusions: it explains why erasing information dissipates heat without making information ``material,'' why quantum superposition is informationally richer than any classical mixture, and why information loss in black holes is physically significant beyond mere bookkeeping. The proposal sits within a structural-realist framework but departs from standard structural realism by locating the relevant structure in modal, not merely actual, relations. I conclude by sketching implications for the foundations of quantum mechanics, quantum gravity, and scientific ontology more broadly.

16.
arXiv (CS.CV) 2026-06-18

DVANet: Degradation-aware Visual-prior Alignment Network for Image Restoration

All-in-One image restoration aims to develop a unified restoration framework for handling diverse degradation types. Existing end-to-end methods usually regard the restoration process as a black-box mapping, lacking an explicit optimization interpretation. Although deep unfolding provides an interpretable iterative modeling paradigm for image restoration, existing methods mostly rely on fixed degradation assumptions or predefined degradation information, making them difficult to adapt to unified restoration requirements under complex degradations and locally damaged content. This limitation restricts their performance in degradation suppression and structural detail recovery. To address these issues, this paper proposes DVANet, a deep unfolding network inspired by the half-quadratic splitting optimization algorithm, which formulates unified image restoration under complex degradations as a collaborative unfolding process between degradation-aware observation consistency and visual-prior-guided reconstruction. Specifically, in the degradation-aware observation consistency branch, a degradation representation module is employed to extract global degradation attributes and local degradation cues, and degradation-conditioned mapping is used to enhance the model's adaptability to different degradation types. In the visual-prior-guided reconstruction branch, DINOv3 is introduced to provide structural and semantic information as hierarchical visual priors, thereby complementing the missing structural information in damaged regions and improving detail recovery. Extensive experiments demonstrate that DVANet achieves superior or competitive performance on multi-scenario degradation and cross-domain image restoration tasks, showing favorable degradation adaptability and generalization ability.

17.
arXiv (CS.CV) 2026-06-12

DuET: Dual Expert Trajectories for Diffusion Image Editing

Recent diffusion editors perform diverse instruction-based edits while conditioning on the source image at every denoising step. Yet persistent source-image conditioning can limit how fully an edit is executed and how natural the result appears, especially when the target scene diverges substantially from the input. We introduce DuET (Dual Expert Trajectories), a training-free inference method that temporarily relaxes source-image conditioning by transitioning through a text-to-image phase before returning to edit mode, allowing the denoising trajectory to move toward the target distribution while retaining the structural benefits of image-conditioned editing. Without modifying model weights or increasing sampling cost, DuET consistently improves instruction relevance, semantic fidelity, and perceptual quality across diverse models and benchmarks. In some cases, these gains come with a modest reduction in source-image preservation, revealing a predictable trade-off between source preservation and edit fidelity.

18.
arXiv (CS.LG) 2026-06-16

SDVDiag: Multimodal Causal Discovery for Online Diagnosis in Software-defined Vehicles

arXiv:2606.15559v1 Announce Type: cross Abstract: The transition toward software-defined vehicles concentrates an increasing share of vehicle functionality into distributed software services, where failures propagate through service dependencies and the surface symptom is often several causal hops away from the underlying defect. Existing approaches to causal root-cause analysis in such systems address this only partially: they typically reason over a single observability modality and operate in an offline, operator-driven mode that does not match the demands of continuous vehicle operation. This paper presents SDVDiag, a multimodal causal-discovery pipeline that fuses log-based and metric-based service representations into a shared embedding space before graph construction, coupled with an anomaly-driven trigger that converts the diagnostic platform from a manually operated batch tool into a continuously running online system. Evaluation on an Autonomous Valet Parking testbed shows that the multimodal pipeline produces sparser causal graphs than a metrics-only baseline (134 vs. 182 edges on average) and consistently outperforms it in edge-weighted reward against an expert knowledge graph at every stage of human-feedback refinement, showing a 2.4-fold improvement over the baseline after 60 feedback queries. An end-to-end fault-injection scenario further demonstrates that the integrated trigger correctly recovers a true root cause located two causal hops upstream of the observable symptom.

19.
medRxiv (Medicine) 2026-06-22

Integration of lung tissue proteomics and genome-wide association data to identify lung cancer susceptibility proteins and potential drug targets

Background: Proteins directly impact disease development and act as drug targets. Therefore, we integrated genomic and lung tissue proteomics data to identify lung cancer susceptibility proteins, elucidating genetic mechanisms and candidate drug targets. Method: We profiled the proteome and genome in non-neoplastic lung tissue from 200 lung cancer patients. Using this data, we constructed genetic models to predict abundance across the proteome in lung tissue. We applied these models to genome-wide association study (GWAS) data from 55,174 lung cancer cases and 1,294,174 controls to evaluate their associations with the risk of lung cancer, overall and by major histological subtypes. Bayesian colocalization and Mendelian randomization (MR) analyses were used to prioritize putative causal proteins, which were cross-referenced with three main drug-protein databases to identify potential therapeutic targets. Results: We identified 29 proteins associated with lung cancer risk at a false discovery rate < 5%, including 25 for overall lung cancer, two (AQP3 and IL18) specifically for adenocarcinoma, and another two (HMGN2 and HLA-DMB) for squamous cell carcinoma. Of them, genes encoding 17 proteins reside at least 2Mb away from any known GWAS risk loci, including 14 for overall lung cancer (HYI, GPX1, GMPPB, DSP, HDDC2, MTCH2, SUOX, JMJD7, PDIA3, IL16, IQGAP1, SULT1A2, ARHGAP27, and TYMP) and three for subtypes (AQP3, IL18, and HMGN2). Among the 12 proteins located within the known risk loci, EPHX2, CLDN18, PSMD5, and CYP2S1 proteins showed an association independent of the proximal GWAS-identified lead variant. Colocalization and/or MR analysis suggested 11 potential causal proteins. Five of these candidate causal proteins (DSP, CLDN18, IQGAP1, IL18 and TYMP) are targeted by nine drugs already approved by the FDA or in phase III trials. Conclusion: Our study identified novel lung cancer susceptibility proteins and potential drug targets, offering valuable insights into lung cancer biology and future translational utilities.

20.
PLOS Computational Biology 2026-06-05

A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity

by Holly A. Huber, Stacey D. Finley Computational models in systems biology are often underdetermined—that is, there is little data relative to the complexity and size of the model. This lack of data is primarily due to limits in our ability to observe specific biological systems and restricts the utility of computational models. To reduce this uncertainty, recent methods have explored augmenting parameter inference of systems biology models with predictions from machine learning models. Such approaches expand the pool of data that is applicable for the inference problem. Here, we explore augmenting the parameter inference of intracellular signaling models. We choose to investigate signaling because experimental measurements of the variables of interest, protein dynamics, are still quite limited. To investigate, we propose a novel, multiscale, Bayesian inference approach that augments traditional signaling data with predictions of binding affinity. These predictions are generated using a machine learning pipeline with measurements of amino acid sequence, from the Universal Protein Resource, or protein structure, from the Protein Data Bank, as inputs. We find that we can successfully integrate these measurements into the inference problem using our novel framework. Excitingly, this integration significantly improves the parameter estimates of signaling models. We demonstrate that how much this improvement impacts predictions of signaling depends on the sensitivity of the prediction to perturbations in the parameter values. Overall, the framework we establish here improves the parameter inference of intracellular signaling models by successfully bridging data on protein sequence and structure with systems-level signaling.

21.
arXiv (CS.CL) 2026-06-17

MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks

Complex medical reasoning requires integrating heterogeneous clinical evidence across multiple inference steps. Large language models (LLMs) now approach this through two routes: internalized reasoning and externalized agent scaffolding (frameworks that decompose problems collaboratively amongst multiple LLMs). To determine whether these routes are exclusive or complementary, we introduce MedicalAgentsBench, a filtered benchmark of 862 complex clinical questions drawn from the union of eight medical datasets via difficulty-aware curation and contamination screening. Evaluating three internalized reasoning models (DeepSeek-R1, o1-mini, and o3-mini), seven base models, and nine externalized agent-based methods, we find that internalized and externalized approaches each independently improve performance, and that their benefits compound: the highest accuracy is achieved by layering agent workflows onto an internalized reasoning model (i.e., o3-mini + MDAgents with 35.1%). Pareto analysis shows this combination dominates the cost-performance frontier; moreover, lightweight optimization on inexpensive models offers an entry point for resource-constrained settings. Our benchmark is at https://github.com/gersteinlab/MedicalAgentsBench.

22.
arXiv (CS.CL) 2026-06-11

Beyond Fully Random Masking: Attention-Guided Denoising and Optimization for Diffusion Language Models

Diffusion large language models (dLLMs) offer an efficient alternative to autoregressive models through parallel decoding, yet existing post-training methods largely rely on random masking strategies that overlook intrinsic token dependencies. In this work, we present an empirical analysis of attention in dLLMs and show that tokens attending more strongly to unmasked context exhibit greater generation stability and play a critical role in reasoning. Motivated by these findings, we propose AGDO, an attention-guided denoising and optimization framework that aligns both training and optimization with attention-derived dependencies. AGDO determines the denoising order based on attention structure and emphasizes attention-critical tokens during supervised fine-tuning and reinforcement learning. Experiments on mathematical and coding benchmarks demonstrate that AGDO consistently improves reasoning performance, outperforming state-of-the-art post-training methods for dLLMs.

23.
arXiv (quant-ph) 2026-06-11

A semi-definite programming formulation of the device-dependent guessing probability

arXiv:2606.12079v1 Announce Type: new Abstract: In quantum mechanics, a measurement applied to a state in general produces some amount of intrinsic randomness. This is not only a fundamental feature of the theory, but is also at the basis of any quantum process to generate random numbers. The simplest of such processes consists of a single, fully charaterized, measurement acting on a single, fully characterized, state. Unfortunately, no general method to estimate the intrinsic randomness produced in such setups is known. In this work, we address this issue by presenting a semidefinite programming formulation of the maximum probability with which an adversary, Eve, can guess the outcomes of characterized but untrusted prepare-and-measure setups. We then present several applications of this construction. First, we apply our method to a variety of specific setups, allowing us both to benchmark the approach and, more importantly, to determine the exact amount of certifiable randomness in scenarios where only upper bounds were previously available. Then, we show that the presence of entanglement between the device preparing the state and the measurement strictly increases Eve's predictive power, already in the most elementary setup of a binary measurement acting on a qubit state.

24.
arXiv (quant-ph) 2026-06-17

Experimental Characterization and Modeling of Measurement-Induced State-Transitions in a Fluxonium Superconducting Qubit

arXiv:2606.17866v1 Announce Type: new Abstract: Superconducting qubits are most often measured using dispersive readout, which, ideally, implements a projective quantum non-demolition (QND) measurement. While a larger readout drive can increase the signal and, thus, reduce discrimination errors in the readout, strong microwave drives may also cause non-QND errors by driving the qubit to a state outside the computational subspace. In this work, we experimentally characterize measurement-induced state transitions (MIST) in a fluxonium qubit over its full external flux range. We further numerically calculate the MIST errors, and find that the theory accurately predicts eleven experimentally identified regions with increased MIST. In addition to transitions to higher fluxonium levels, we also find that, at certain flux points, MIST errors are dominated by transitions that include the transmission-line-like array modes of the fluxonium's superinductor. The excellent match between theory and experiment validates that the models accurately predict the occurrence of MIST in these systems, and further highlights the influence of array modes in fluxonium readout.

25.
arXiv (CS.LG) 2026-06-18

INDEQS: Informed Neural controlled Differential EQuationS

arXiv:2606.19138v1 Announce Type: new Abstract: Neural Controlled Differential Equations (NCDE) provide a powerful continuous-time framework for forecasting time series, but standard graph-based extensions typically learn spatial structure purely from data, even in settings where a directed graph structure is known a priori. We introduce Informed Neural controlled Differential EQuationS (INDEQS), a graph-based NCDE forecasting method that incorporates prior knowledge of a directed graph at distinct architectural positions. INDEQS separates inner mixing of hidden states across graph nodes from outer mixing between vector field and control, and offers both a lightweight graph-constrained variant and a more expressive variant, learning additional graph connections from data via adaptive graph convolutions. To systematically study when graph informedness is beneficial in forecasting, we devise a continuous advection simulation on directed graphs, yielding synthetic spatio-temporal datasets with known ground-truth flow structure. We then evaluate INDEQS on two real-world tasks: river discharge forecasting on a hydrological network and traffic flow prediction on PeMS08. Across these synthetic and real-world benchmarks, outer informedness consistently improves mean absolute error over an uninformed NCDE with comparable parameter count, particularly on larger graphs, while inner informedness offers a more parameter-efficient alternative when strict adherence to a known adjacency is desired. A comparison of discrete convolutional and continuous-time decoders further shows that continuous decoders yield better accuracy and greater temporal flexibility on real-world tasks. An implementation of INDEQS and the advection simulation is available at https://github.com/Mitchi1/indeqs.